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An anonymous reader brings word of a new application for PageRank, Google's link analysis algorithm: monitoring the food web in an ecosystem. A team of researchers found that a modified version of PageRank can predict with great accuracy which species are vital to the existence of others. Quoting:
"Every species is embedded in a complex network of relationships with others. A single extinction can cascade into the loss of seemingly unrelated species. Investigating when this might happen using more conventional methods is complicated, as even in simple ecosystems, the number of combinations exceeds the number of atoms in the universe. So, it would be impossible to try them all. Co-author Dr. Stefano Allesina realized he could apply PageRank to the problem when he stumbled across an article in a journal of applied mathematics describing the Google algorithm. 'First of all, we had to reverse the definition of the algorithm. In PageRank, a web page is important if important pages point to it. In our approach, a species is important if it points to important species.'"

Pagerank is just a repeated application of a transformation matrix. It has the effect of running a Markov model (a way to model discrete states) until there is convergence. He just used a Markov model the way that it is supposed to be used...

We're finally able to figure out what species will have the most impact if it is removed. Likely, the folks at google are turning this into some sort of biological warfare device - They want to figure out which species of mosquito we have to kill in order to remove all mouth-breathers from the planet, leaving all the hot women alive for the rest of us.

More seriously, if we can figure out which species are most important (and which are least important), doesn't that give both the tree-hugging sea-kittens a

Likely, the folks at google are turning this into some sort of biological warfare device - They want to figure out which species of mosquito we have to kill in order to remove all mouth-breathers from the planet, leaving all the hot women alive for the rest of us.

Actually the Markov model is prevalent in bioinformatics, as well as other statistical methods. However, the biologists are an entirely different race, typically unfamiliar with advanced mathematics. In fact, the entire field of biology works on foundations and culture so alien to science (fondness for objectivity and modesty) sometimes I wonder whether it is right to call them scientists, or just group them with the social scientists and psychologists.

In fairness to biologists, their science has only recently (compared to other sciences) become a "hard" science with strong foundational theories and strongly determinant principles that could be applied to arrive at a conclusion. Largely, it still is in the fuzzy region between the hard sciences (like physics and astronomy) and the social sciences (like anthropology and psychology). I've even seen biologists use anthropological tools and study methods when investigating animal behavior, to give an exampl

On the other hand, I've seen biologist written perl code [oxfordjournals.org] that terminated on div-by-zero, and closed, re-opened then seeked into the input file rather than implement a linear processing of data. I've also met plenty of biology grad students who basically said their technique for analysis was to invite a statistics co-author. If you're going to claim Mendel as a mathematical biologist, we might as well call Babbage a computer scientist, and he built the diffrence engine 30 years before Mendel's pea experiment

Because it's a novel use of an existing method? It was published in PLoS and not some mathematics journal. So, while the algorithms are not new, they may be new to the intended audience. The actual claim of the article is that it can offer a predictive analysis of extinction rates of a species and validated them on some in-silico experiments. This could be useful for bench-scientists, as they could figure out what might happen in an experiment before running expensive tests. This might be useful for conservations trying to make sure whole ecosystems don't die out due to the removal of a species; the 'might' is significant as real-world ecosystems are generally more complex. But anyways, it's interesting because the models have practical application outside of theory to help us understand the world.

Yes, it is notable that this wasn't published in 'some mathematics journal'. Pagerank is computing the limiting distribution of a discrete-time markov chain applied to webpages using a certain statistical model of hyperlinks. It makes no sense to talk of applying 'pagerank' to things other than webpages, because that's what makes pagerank special! As soon as you take pagerank out of the web-context, it's just a steady state analysis of a markov chain, which is a standard statistical technique covered in undergraduate statistics courses. It's like saying applying bayesian inference to a problem in ecology is using a 'spam filter.'

For me, this tells me that perhaps these researchers should wander over to their local mathematics department more often. They might find all sorts of goodies that mathematicians have developed in the past few centuries. Dr. Allesina might have discovered that there was no need to reverse engineer the algorithm, since the underlying mathematical principles have been well understood for over a hundred years. We might have a better understanding of the world if most sciences took mathematical models as seriously as physicists do.

Quite so. The problem with PageRank is that it's quite a crude
approach to simulation, in fact. The steady state distribution is just
an average, whereas we already understand how to do so much more, eg
looking at the sizes of random fluctuations and maxima and minima.

It would be good if these biologists who are impressed with this example
were to read a book about Markov processes, or took a postgraduate course in
stochastic processes. This isn't rocket science, it's quite commonly used by
engineers, phy

No, you're right. It's not notable. Whenever one area of knowledge is improved, every other area is instantly aware of this discovery and can utilize it with 100% efficiency right away.

Less sarcastically, I am not surprised a biologist is unaware of such mathematical models. It's notable for the fact that they're applying a rather simple method to a rather old problem and it's extremely effective.

Yeah, I would tend to call BS on that particular statistic. Let's say the average water bottle is.5L. In that one, single water bottle that is sitting on my desk, there are 5.01*10^25 atoms. That's one hell of a number.

Now, let's pretend God has a really good magnifying glass and a really small set of tweezers, and he's removing atoms from this water bottle at a rate of 1 per second. Conservative estimates put the universe at 13.5 billion years old, which converts to 4.25*10^17 seconds.

What does your tweezers and removing atoms have to do with combinations? It is trivial to come up with a situation where there are more possible combinations that atoms of the universe. The number of possible chess games starts to get close (magnitude of 50 versus 80 for the atoms in the universe. Slightly more complex scenarios would easily go past 10^80. The trick is to find a way to model the complexity with a much simpler algorithm.

We are humans. Really humans are the only species that in the end matter. So long as we have enough food and oxygen, all is good and the survival of our species is guaranteed (assuming no effects of huge disasters such as an asteroid impact, etc.)

Please tell how you think we are currently becoming overpopulated? For one we have enough food to feed -everyone- the problem is corrupt government and lack of education that causes hunger in third-world countries. In first world countries its quite easy to get food and shelter so no one should ever die of hunger. Yeah, you won't be eating steak and shrimp every night, but you aren't going to starve to death. Take a drive to North Dakota sometime if you don't think we have enough space. If you read the UN's

If you're under 40 and in good health you're in for a rather rude awakening, with those beliefs. You'll likely live to see the shit begin to hit the fan in a serious way. Google and other online sources should be education enough for you. I'm too disorganized to do anything more than plant the seed; you'll have to water and feed it.

So lets see here, I'm supposed to believe some random person on the internet because of A) Sci-Fi films, B) "facts" that contradict reputable sources such as the United Nations and C) ideas that don't make much sense. Lets see here, we have technology that allows us to grow more crops in a single area than ever before, technology that lets us grow more crops with less effort (we have less humans employed as farmers than before yet have more crops than before) and technology that will let us grow crops in pl

Let's start with a car analogy: You tell me that things in the mirror may appear closer than they actually are... to which I respond "Who the hell looks in their mirrors"?

I'm guessing you've never watched 'Silent Running', but given what you said you might wanna start your re-education with another old movie: 'Soylent Green'.

I think you need to re-educate yourself with another movie: The Omega Man. If that's where we'll end up anyways, who cares how we get there? Eat drink and be merry, I say. Isn't there some movie about people being brainwashed with media and living in a world that isn't real (but they think it is) because they're too plugged into modern cu

Seriously, "so long as we have enough food and oxygen, all is good" ? Where the fuck does that food come from, idiot ? What processes combine to create that food ? Which lifeforms are necessary to provide those processes ? Which out of the millions of bacteria is it safe to eliminate before we are unable to digest food at all ?

I suppose you think fossil fuels are good because they are effectively free, all you have to do is dig them up. And that is relevant, as without fossi

Guess who actually got modded as Troll, though? Nope, not the "idiot"... it was my original comment pointing out the larger context being ignored (for the sake of TOFA). Modded as Troll not just once, but repeatedly.

If there's one thing about Slashdot that should change, it's the removal of anonymity when people moderate.

In PageRank, a web page is important if important pages point to it. In our approach, a species is important if it points to important species.'"

The difference is, its pretty obvious to a human if a page is important. On the other hand there are a lot of species that we don't know if they are important or not. So how do we know what the "important" species are? Other than humans, we don't know of any real "important" species. Could the ecosystem survive without X? Theres no way we can really know that.

Well of course, we know that above all things nature simply survives. But we can't know for certain whether they are "important" for it to survive on its own. Especially with the ever-changing nature of the world. If a predator dies will another predictor eaten by the other predator move in? Will the prey multiply like crazy? Its these things that will make the PageRank algorithm useless in biology.

The model helps determine if a species is important. That's the whole point. Previously, we didn't have an easy way to determine a particular species impact on an ecosystem until it was almost extinct or already gone. Now by using "PageRank" to determine their importance, we can model what will happen if specific species are no longer part of the food web.

I was worried about this. Either underspecifying "importance" or using it in a simplistic way (though you may not actually be doing these things).

It measures a kind of importance. Not importance in all respects. Specifically, it measures importance in interdependence. Which only very roughly translates to an idealized general or universal importance.

Remove humans from the web and you won't get much "impact on [the] ecosystem" (in the form of cascading die off). Yet humans are generally regarded as "imp

The idea of saving an animal based on its appearance is one of the reasons why many animals receive a disproportionate amount of funding. There are some species of animals that have more money diverted to them than hundreds of other species combined for no other reason than they are more marketable.

If pandas go extinct, what effect would it have on the ecosystem? Almost none. It eats bamboo for 99% of its diet and I doubt it eats enough to be a source of control on the growth of bamboo. However, pandas are

The plumage comment was a joke, sorry. I was trying to be ludicrously shallow, but the truth is that beauty actually does count for something.

The value of life is not simple, so it's not easy to put it simply. For example, it's not clear to me what "good for the ecosystem" means. It sounds like maybe it means "tendency to preserve the extent (quantity?) of food/consumer relationships" or maybe "tendency to preserve maximal living mass" or maybe "tendency to promote diversity". This is real philosophical

I've often been annoyed by the excessive focus on the iconic [washingtonpost.com] and popular species in many endangered species awareness campaigns. It is easy to say "we are spending a million dollars on protecting a worm?" in Congress, but when more renowned species like a hammerhead shark variety are endangered, they will naturally get more attention. Now scientists can defend their case for funding by pointing to this algorithm.

whats wrong with low prices? would you prefer high prices so people can't invest in cleaner technology eg. i can't afford that prius because the cost of living means i'm JUST scraping by. i think there is a hole in your thinking there.

People generally don't want to spend their money saving some worm. As it's been suggested before, the focus on megafauna partly exists just because they are charismatic. Panda bears are fricking cute. And people will donate money to save panda bears, their habitat, and everything else living there. It's unfortunate, but it's just facing the reality of the situation. Being able to identity the real keystone species would be great for the actual scientists, conservationists, and policy makers. But when its ti

Ok, Captain Expert. Pagerank is awful, and that's why Google is not useful to anyone. And these people trying to apply it to what organisms eat other organisms -- not, as you seem to think, to what restaurants are better than others -- is completely moronic as well, since the quality of the organisms' meals are more important than what organisms depend on what other organisms and to what extent, which these poor mislead people are paying attention to.

I'd expect McDonald's to be ranked very high based on importance to the diets of people around the world while the importance of, say, filet mignon to be comparatively negligible. There are times where a popularity contest works: "Hey, people are getting fat. What food should we make healthier? Well, people seem to be eating a lot of hamburgers, so lets see if we can make those leaner!"

Pagerank isn't an important algorithm, it's an application of an important mathematical concept. Pagerank is just computing the limiting distribution of a specially constructed Markov chain, which is very important and has many applications beyond pagerank and 'popularity contests.'

At the heart of Pagerank is the idea that, if one has a connection matrix between 'things' and these connections are related to the scoree, one can pose the problem as an eigenvalue problem [wikipedia.org]. That's a pretty cool insight, and is applicable to many more fields than internet searches, for instance: ranking articles due to citations, teams based on wins and losses, and now finding important species based on their genetic connections.

I would imagine that the many places Pagerank has found application would c

It's a pity that this insight isn't Google's insight. It's been known for a hundred years, and goes back to the works of A.A. Markov, G. Kirchhoff, O. Perron and F.G. Frobenius (look them up on wikip).

The *only* thing worthy of note with PageRank is the humongous size of
the graph that is being modeled. This could never have been attempted
until the 1990's because computers weren't powerful enough before (and
the few that were just weren't going to be used for "silly" things like
web search).

Meaning it is not new as a method by itself, but applying it to the linking-structure of the WWW in order to producerelevant documents for a query, was new. I think it is fair to say that the Google Pagerank matters very little, outside of being able to rank otherwise
not-comparable search results.

And so it is better to state that "a specialized Eigenvector Centrality Measure can predict with great accuracy which species are vital to the existence of others" instead of "a modified version of PageRank can predict with great accuracy which species are vital to the existence of others". One can see that also when one realizes that these biologists have no query, no search, no equivalent of search keywords.

On the other hand, when the post says "Co-author Dr. Stefano Allesina realized he could apply PageRank to the problem when he stumbled across an article in a journal of applied mathematics describing the Google algorithm." -- I guess he might have found the method through the Google name.

Certainly this is an additional tool that can be used to explore Lovelock's Gaia hypothesis. If other elements were included in the web of interactions such as atmospheric and dissolved CO2, the actions of rocks it might provide a further insight into global warming and what we should be looking at the mitigate it.